Is it possible to set a timeout for an SQL query on Microsoft SQL server?

As far as I know, apart from setting the command or connection timeouts in the client, there is no way to change timeouts on a query by query basis in the server.

You can indeed change the default 600 seconds using sp_configure, but these are server scoped.

Humm! did you try LOCK_TIMEOUT
Note down what it was orginally before running the query
set it for your query
after running your query set it back to original value

SET LOCK_TIMEOUT 1800;  
SELECT @@LOCK_TIMEOUT AS [Lock Timeout];  

In management studio you can set the timeout in seconds. menu Tools => Options set the field and then Ok